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DNA Stable Isotope Probing to Examine Organisms Involved in Biodegradation

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Microbial Metabolism of Xenobiotic Compounds

Part of the book series: Microorganisms for Sustainability ((MICRO,volume 10))

Abstract

In situ applications of molecular biology to terrestrial and aquatic ecosystems have advanced the study of activities of microorganisms without the need for cultivation. DNA-based fingerprinting tools, such as 16S-TTGE, T-RFLP, DGGE, or pyrosequencing, facilitate in assessing pesticide impacts on microbial community composition. Quantitative PCR or functional gene microarrays help us understand effects of pesticides on genes of interest. Such tools improve our understanding of environmental impacts on microbial phylogeny or function, though few can link a specific organism to its function in situ. Stable isotope probing (SIP) emerged specifically to provide this linkage. SIP approaches vary in sensitivity, specificity, and inference space, depending on biomolecules targeted to obtain phylogenetic information. Combining SIP with “omics” tools further characterizes responses of microbial communities to environmental events. Herein we have reviewed strengths and weaknesses of common SIP techniques, with emphasis on the ecology of pesticide degradation.

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Authors and Affiliations

  1. Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, USA

    Gerald K. Sims

  2. Department of Animal Science, University of Minnesota, St. Paul, MN, USA

    Andres M. Gomez

  3. Southwest Florida Research & Education Center, University of Florida, Immokalee, FL, USA

    Ramdas Kanissery

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  1. Gerald K. Sims
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  2. Andres M. Gomez
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  3. Ramdas Kanissery
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Correspondence to Gerald K. Sims .

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  1. Department of Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India

    Pankaj Kumar Arora

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Sims, G.K., Gomez, A.M., Kanissery, R. (2019). DNA Stable Isotope Probing to Examine Organisms Involved in Biodegradation. In: Arora, P. (eds) Microbial Metabolism of Xenobiotic Compounds. Microorganisms for Sustainability, vol 10. Springer, Singapore. https://doi.org/10.1007/978-981-13-7462-3_3

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